[Bioperl-l] Bio::Variation::RNAChange

Heikki Lehvaslaiho heikki at sanbi.ac.za
Sun Jul 8 03:32:21 EDT 2007


On Friday 06 July 2007 17:43:41 Nathan S. Haigh wrote:
> Heikki Lehvaslaiho wrote:
> > Hi Nat,
> >
> > These modules have not been touched for a while and were developed for a
> > specific task. A revire is defiitely in order.
> >
> > The way RNAChange->label was written, it should return 'inframe' when
> > given no alleles, but 'no change' would actually be better.
>
> Wouldn't this effectively be changing the API since past scripts "could"
> expect "inframe" to be returned.

Checking tha actal usage and what happens when you do change of a nucleotide 
to itself, you get the label 'silent'. I guess that would be a valid lable 
value even when the alleles are not initialised, too.

> > The multiple alleles were originally though to be a good idea, but the
> > vocabulary for labels was developed for single allele, only, The use of
> > the module ended up being limited to single allele, so add_allele()
> > behaviour was conveniently ignored but not removed. :(
>
> So add_Allele() and each_Allele() should be deprecated in favour of
> allele_mut()?

Yes.

> From my post about API's.....how should the capitalisation of
> add_Allele() and each_Allele() be changed?

Definitely, keept the current ones as deprecated alternatives.


    -Heikki

> Cheers
> Nath
>
> > 	-Heikki
> >
> > On Friday 06 July 2007 14:54:33 Nathan S. Haigh wrote:
> >> Nathan S. Haigh wrote:
> >>> I'm taking a look at the tests for Bio::Variation::RNAChange.
> >>>
> >>> If you create a new oject without arguments:
> >>> my $obj = Bio::Variation::RNAChange->new();
> >>>
> >>> What do you expect the following to return:
> >>> $obj->label();
> >>>
> >>> I thought it would probably be:
> >>> 'inframe'
> >>>
> >>> However you get:
> >>> 'inframe, deletion'
> >>>
> >>> Can anyone in the know explain what behaviour would be expected?
> >>>
> >>> Cheers
> >>> Nath
> >>
> >> Following on from this, AAChange has the following two methods:
> >> add_Allele() and allele_mut()
> >>
> >> It appears that allele_mut is only capable of remembering 1 allele at a
> >> time, whereas add_Allele() is provided to add support for mutliple
> >> alleles - is that correct?
> >>
> >> However, add_Allele() also calls allele_mut(), such that mutliple calls
> >> to add_Allele will result in the overwriting of the allele being
> >> remembered by allele_mut(). Things are further complicated by the fact
> >> that label() uses allele_mut() to decide on the label to return.
> >> Shouldn't label know aout multiple alleles set by multiple calls to
> >> add_Allele?
> >>
> >> It may be my lack of understanding alleles and what these classes are
> >> intending to do, but trying to rewrite the test scripts to improve code
> >> coverage has let me a little confused!
> >>
> >> Thanks
> >> Nath
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


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